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Germs come clean

Georgia Tech Professor Kostas Konstantinidis displays Shewanella microbes that have the ability to "inhale" certain metals and compounds and convert them to an altered state, which is typically much less toxic.

Using genetic analysis, scientists discover that a type of germ used for cleaning up toxic sites is actually many types of germs that gobble up different kinds of crud. This suggests that a smorgasbord of microbes could be customized for different applications – ranging from cleaning nuclear dump sites to powering future fuel cells.

"Soon we will be able to pick the right strain for cleaning specific environments," said Kostas Konstantinidis, an environmental microbiologist at Georgia Tech. "But we are in the beginning stages of this."

Konstantinidis and his colleagues focused on a bacterial genus known as Shewanella, which is found in a wide spectrum of ecosystems ranging from the Arctic to the Amazon. Their genetic analysis of 10 strains of Shewanella is being published online this week in the Proceedings of the National Academy of Sciences.

Shewanella typically converts metals and other nasty compounds into less toxic stuff - which makes the bacteria well-suited for environmental cleanup duty. One strain of the bacteria, Shewanella oneidensis MR-1, is particularly good at sucking metal oxides from groundwater and transforming them into insoluble forms that are ripe for removal. The Energy Department is looking into whether that strain could help clean up radioactive nuclear weapons sites.

One of Shewanella's strengths is that it adapts easily to different environments and energy sources. "They can actually capture DNA from the environment that gives them a selective advantage," said Margaret Romine, a researcher at the Pacific Northwest National Laboratory and one of Konstantinidis' co-authors.

In the lab, one strain of Shewanella can look just like another - which is a problem if you're trying to find just the right germ for the job.

"If you look at different strains of Shewanella under a microscope, or you look at their ribosomal genes, which are routinely used to identify newly isolated strains of bacteria, they look identical," Konstantinidis explained in a Georgia Tech news release. But when 10 seemingly similar strains were subjected to whole-genome sequencing and proteomic analysis, the researchers found far more diversity than they expected.

Some strains had 98 percent of their genes in common, while others shared only 70 percent of their genes. And the differences in expressed proteins were even larger than the differences in genetic content. In comparison, humans and chimpanzees have 96 percent of their genetic coding in common.

"In humans, there are multiple levels of organization, so it's not fair just to compare the numbers," Konstantinidis told me. "But it does give you a perspective on how much diversity exists there in the environment."

All but one of the 10 strains studied could gobble up several types of metals. The oddball was a type of bacteria that couldn't convert metals anaerobically, but relied on nitrates and oxygen instead. "There are a lot of things that this one guy has lost, so what it's done is that it's taken a different evolutionary path," Romine said.

The genetic analysis indicated that the Shewanella strains acquired the genes that were needed to adapt to a particular environment - freshwater or saltwater, sandstone or sediment - and shed the genes that became unnecessary.

Konstantinidis said the kind of genetic analysis he and his colleagues conducted could eventually serve as a guide for finding "the right strain for the right environment in the right conditions."

In the short term, scientists could mix up a smorgasbord of Shewanella and see which strains worked best in which setting, Konstantinidis said. In the longer term - say, five years from now - scientists could well be making genetic modifications to customize bacterial strains for a particular cleanup job or energy application.

That may sound like a bioengineering dream come true - and in fact, there are signs that we're already well on our way toward a biotechbounty. But in the wrong hands, genetically engineered bacteria could spark a bioterror nightmare. What do you think? Feel free to weigh in with your comments below.

The research reported in the Proceedings of the National Academy of Sciences was supported by the Energy Department through the Shewanella Federation consortium and the Proteomics Application project. In addition to Konstantinidis and Romine, the research team included Margrethe Serres of the Marine Biological Laboratory at Woods Hole, Mass.; Jorge Rodrigues of the University of Texas; Jennifer Auchtung and James Tiedje of Michigan State University; Anna Obraztsova and Kenneth Nealson of the University of Southern California; Carol Giometti of Argonne National Laboratory; and Lee-Ann McCue, Mary Lipton and James Fredrickson of the Pacific Northwest National Laboratory.